GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Nocardiopsis gilva YIM 90087

Align glucose transporter, ATPase component (characterized)
to candidate WP_026126106.1 CDO52_RS22210 ATP-binding cassette domain-containing protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_002263495.1:WP_026126106.1
          Length = 270

 Score =  192 bits (489), Expect = 5e-54
 Identities = 107/239 (44%), Positives = 152/239 (63%), Gaps = 9/239 (3%)

Query: 13  TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72
           TPL+E   +   +G + A+D   ++LYPGE++ ++G NGAGKSTLIK LSGA   D GEI
Sbjct: 13  TPLLEAHGLVKRYGRVTALDGTDLELYPGEILAVIGDNGAGKSTLIKCLSGAVVPDEGEI 72

Query: 73  RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTP------FGLVDD 126
           R++G  V +  P  ARS  IET++QTLA++ +LD ASNLFLGREL  P      F  +D 
Sbjct: 73  RLDGGPVRLDTPLAARSAGIETVHQTLAVSPSLDIASNLFLGRELRKPGVVGAVFRTLDH 132

Query: 127 SAMEAECRKIMNRLN-PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG 185
             M  E  + ++ L     Q   + V  LSGGQRQ+VA+ARA  F ++++IMDEPTAALG
Sbjct: 133 KRMREEALRHLDALGVMTIQNPGQAVETLSGGQRQAVAVARAAAFGSRVVIMDEPTAALG 192

Query: 186 PHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDID--DVTD 242
             E+  V +LI +++  G+ + +I H++  V E+ DR  + + G+ V TV  D  D+TD
Sbjct: 193 VRESHAVLDLILRVRESGLAVIVISHNMPHVFEIADRIHIQRLGRRVATVTPDECDMTD 251


Lambda     K      H
   0.317    0.135    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 184
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 270
Length adjustment: 25
Effective length of query: 235
Effective length of database: 245
Effective search space:    57575
Effective search space used:    57575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory